CD molecule information (NIH)

Common cell surface markers are the following:

CD3 which is a T cell receptor coreceptor. 

CD4 molecule is a relatively non-polymorphic, 55 kDa surface glycoprotein comprised of four extracellular domains, a hydrophobic transmembrane region and a hydrophilic cytoplasmic tail. The NH2 terminal extracellular domain (V1) has striking sequence homology to Ig light china variable retions. The other extracellular domains (V2-V4) are hoologous to other members of the Ig gene superfamily. CD4 is expressed mainly on T helper lymphocyte subsets which recognize peptide antigens bound to Class II MHC molecuels. The NH2 erminal domain of CD4 also contain binding residues most important in the interaction of CD4 with gp120, the envelope glycoprotein of HIV. (Lederman “A single amino acid substitution in a common african allele of the CD4 molecule ablates binding of the monoclonal antibody, OKT4” Molecular Immunology, 28(11) pp. 1171-1181, 1991). 

CD11a is a member of the ?2 family.

CD11b is a member of alpha-chain integrin and form a complex with alpha2-integrin as Mac-1. CD11b is expressed on neutrophils, monocytes, NK cells and a subset of CD8+ T cells. It plays a central role in mediating migration of leukocytes from peripheral blood to sites of inflammation during the process of host defense. It contributes to form leukocyte adhesion, not only to the endothelium via the but also to the underlying subendothelium and interstitial extracellular matrix by binding diverse kinds of ligands, such as fibronectin, collagens, and laminins. CD11b is a marker that defines and indicates cellular electated levels of activated neutrophils, activated monocytes, activated T-lymphocytes, activated basophils and/or activated mast cells. 

The catechin, EGCG decreases flow cytometric CD11b expression on periopheral blood CD8+ T cells as a fesult of binding to CD11b. 

• CD11c is a member of the ?2 integrin family.

CD16 which is a receptor present on  for the Fc region of IgG.

CD20: (also called human B-lymphocyte-restricted idfferentiation antigen or Bp35) is a hydrophobic transmembrane protein with a MW of aobut 35 kD located on pre-B and mature B lymphocytes. CD20 is found on the surface of more than 90% of B cells from peripheral blood or lymphoid organs and is expressed during ealry pre-B cell development and remains until plasma cell differentiation. CD20 is present on both normal B as well as malignant B cells. In particular, CD20 is expressed on more than 90% of B cell non-Hodgkin’s lymphomas (NHL) but is not found on hematopoietic stem cells, pro-B cells, normal plasma cells or other normal tissues (US2009/0162352). 

CD24 (Heat-stable antigen or HSA) is a small glycosyl-phosphoinositol-anchored cell surface protein that is able to provide costimulatory signals to T cells and has been implicated in the development of autoimmune disease. However, CD24 in association with Siglec10 has been shown to selectively repress inflammatory response to danger associated molecular patterns (DAMPs). CD24 has no known mechanisms for signal tranduction and its anti-inflammatory response is due to the fact that siglecs are cell surface receptors which can interact with CD24 (US 8,163,281). More than 90% of the mass of CD24 is stimated to be derived from glycosylation.

CD35 (CR1) which is a  receptor present on B cells

CD25 is considered a marker of activation.

CD28 which is a T cell receptor for  B7 molecule on an antigen presenting cell. CD28 is a disulfide-linked homodimer on the surface of T cells which binds to members of the B7 family on APCs and costimulates T cell activation. In humans, all thymocytes and the vast majority of cord blood CD8+ T cells express CD28. The proportion of CD8+ T cells that lack surface epxression of CD28 increases with age, so that in adulthood, 25-50% of CD8+ T cells are CD28-. In advancing HIV infection, more than 50% of CD8+ T cells are CD28-. CD25+ phenotype suggests central membory cells.

CD29 is a ?1-integrin. 

CD30 is a member of the .

CD40 along with TNF? is involved in the differentiation of DCs from CD34+ bone marrow or cord blood progenitors. CD40 is expressed on. Its ligand, CD40L, is expressed on . The interaction between CD40 and CD40L increases DC survival, upregulates MHC and costimulatory molecule expression, and induces the expression of a variety of cytokines (e.g.,) in DCs. CD40/CD40L-mediated contacts between B and T cells are required for the generation of T cell-dependent humoral immune respones. Activation of CD40 on B cells stimulates proliferation and mediates Ig class switching in conjunction with IL-4 and Il-13.

CD44: is the major receptor for hyaluronan.

CD45RA is expressed on both naive and antigen-primed effector CD8 T cells.

CD45RBlow express the phenotype of antigen-experienced cells.

CD45RO is expressed predominantly on activated CD8 T cells. Thus CD45RO is usually associated with cells that have experienced antigen and are often referred to as memory cells.

CD58 is a co-stimulatory molecule which has recently been shown to stimulate the production of IL-10 by human T cells.

CD62L L-selectin expression is down-regulated upon activation.

CD66: family members appear to play a role in a wide variety of normal and pathological processes. CD66 monoclonal antibodies (mAbs) react with members of the carcinoembryonic antigen (CEA) family. In the CD terminology, mAbs belonging to the CD66 cluster are classified according to their reactivity with each family member, as indicated by a lower case letter after “CD66” as follows: CD66a, CEACAM-1 or biliary glycoprotein (BGP); CD66b, CEACAM-8 or CGM6; CD66c, CEACAM-6 or NCA; CD66d, CEACAM-3 or CGM1; CD66e, CEA and CD66f, preganancy specific glycoprotein (PSG).

CD69 is considered an early activation marker. 

CD70: costimulates CD4+ T cells to produce IL-2 and IFNy and cross0linking of CD70 also upregulates the expression of CD154 on activated T cells.

CD89 (FcalphaR1): is a membrane glycoprotein that contains two extracellular Ig like domains (206 aa), a membrane spanning region (19 aa) and a cytoplasmic tail (31 aa). Like other Fc receptors lacking an intracellular signaling motife, CD89 signaling into the cell is initiated via its association with the FcRgamma-chain. The FcRgamma-chain is a homodimer signaling unit with a size of 10 kDa. Binding to CD89 leads to phosphorylation of the intracellular, immunoreceptor tyrosin based activation motif (ITAM) on the gama chain, activating the signaling pathways downstream.

CD89 binds both the monomeric and dimeric forms of IgA1 and IgA2. It is expressed only by myeloid cells, including neutrophils, monocytes, macrophages, and eosinophils.

CD93 (C1qRp): is a type 1 transmembrane glycoprotein located on chromosome 20 in humans. It is composed of 652 amino acids including leader sequence, c-type carbohydrate-sensing domain, 5 EGF-like domains, mucin domain, one transmembrane domain and an intracellular domain of 47 amino acids. CD93 is expressed in myeloid lineages, hematopoietic stem cells, NK cells, platelets, microglia and endothelial cells. Human CD93 is a receptor for complement component 1, subcomponent q phagocytosis (C1qRp). It was originally reported to be involved in the C1q mediated enhancement of phagocytosis in innate and adaptive immune response. 

A soluble form of the CD93 that retain the N terminal carbohydrate recognition domain and the epidermal growth factor repeats after ectodomain cleavage has been detected in human plasma (Bohlson, J. Immunology, 2005, 175: 1239-1247) and well as in synovial fluid from rheumatoid arthritis patients (Young, WO/2010/087594; US 13/146876). 

CD95 indicates a memory pehnotype.

CD122 (IL-2 receptor beta chain)

CD137 (4-1BB): is a membrane glycoprotein that is inducibly expressed on activated T cells, B cells, DCs and NKs. It is a member of the TNFR superfamily of costimulatory molecules. Stimulation of CD137 by its natural ligand, CD137L, or by agonistic antibody induces vigorous T cell proliferation and prevents activation induced cell death. The intracellular biochemical pathway for CD137 signaling is not fully understood, but TNFR associated factors (TRAF) 1 and 2 are believed to play a role. CD137-induced signals lead to the recruitment of TRAF family members and activation of several kinases, including ASK-1, MKK, MAPK3/MAPK4, p38, and JNK/SAPK. Kinase activaiton is then followed bythe activation an nuclear translocation of several transcription factors, including ATF-2, Jun, and NF-kB. Anti-human CD137 antibodies are potential biotherapeutic agents to shrink solid tumors in vivo and prevent their recurrence.

CD152 (CTLA)-4: is a high affinity counterreceptor of B7-1 and B7-2 that delivers a negative signal and inhibits T cell proliferation, IL-2 production and cell cycle progression.

CD200 (OX-2): is a highly conserved type I transmembrane glycoprotein expressed on the surface of numerous cell types including B cells, some T cells and DCs. The protein interacts with its receptor CD200R which is largely restricted to cells of the myeloid lineage, including monocyte macrophages, DC, and microglia as well as CD4+ T cells, especially polarized Th2 cells. There are at least two potentially activaitng isoforms of the receptor, designated mCD200RLa and mCD200Lb which do not bind to CD200 and have unknown ligands, but, in common with other receptor pairs, they have potential activating function through DNAX-activating protein-12 (DAP-12) adapter protein binding. The CD200:CD200R interaction has been thought to deliver an immunodulatory signal to cells and induce immunosuppression including apoptosis-associated immune tolerance.

While certain reports show that CD200 has the capacity to modulate myeloid cell activity in an inhibitory manner and delivery and inhibitory signal, other reports have shown that CD200, which has sequence homology to B7.1 and B7.2 molecules, functions as a co-stimulatory molecule to induce T cell proliferation. Thus similar to other described negative co-receptors, CD200 may exert different effects at different points in the immune response.

The CD200R is structurally related to CD200, located on the same chromosome and the genes probably evolved by gene duplication. CD200R is distinct in that it displays a longer cyoplasmic tail containing three conserved tyrosine reisudes, one of which is contained with an NPXY motife. Upon ligand or agonist antibody binding, CD200R is phosphorylated on the tyrosine of the NPXY motife and subsequently binds adapter proteins Dok1 and Dok2. Phosphorylation of these adapter proteins recruits SHIP and RasGAP, which subsequently inhibits the Ras/MAPK activation pathways.

Activation Markers

CD62L, CCR7, CD45RA and CD28 are present on naive cells. Cells which no longer express these cell surface markers have been previously activated.

CD45RO, granzyme A and bcl2 are not found in naive cells.

Introduction:

The term prokaryote describes a cell type or collectively the organisms in the Domains Bacteria and Archaea. The two prokaryotic domains, Arcahe and Bacteria, are not closely related, although both are prokaryotes. In many ways, archae resemble eukaryotes more closely than they resemble bacteria. 

True multicellularity, in which the activities of individual cells are coordinated and the cells themselves are in contact, occurs only in Eukaryotes and is one of their major characteristics. Bacteria and many single-cell Eukaryoties form coloney aggregates of many cells, but the cells in the aggregates have little differentiation or integration of function. 

Bacterial genomes consist of nucleoids (about 4 million base pairs) and 1-50 plasmids (about 1500 base pairs) per cell. Plasmids are almost always circular and replicate independently. They commonly code for genes which confer antibiotic resistance. 

Structure/Differences with Eukaryotes:

Although all replicating cells share the common characteristics of having ribosomes, cytoplasm, a plasma membrane and DNA, there are important differences between eukaryotic and prokaryotic cells. With few exceptions, prokaryotes are single celled. Prokaryotes lack a membrane bound nucleus; instead they usually have a single circular chromosome made up of DNA and histone like proteins in a nucleoid region of the cytoplasm. Prokaryotic cells also have smaller circular DNA molecules called plasmids, which typically confer some selective advantage but are not essential. Cell division in prokaryoties takes place mainly by binary fission instead of by mitotic or meiotic cell division. Prokaryotes also do not have extensive membrane bound organelles like eukaryotes. Most bacteria and archaea have cell walls that confer shape and rigidity upon the cell and pevent cell lysis due to high osmotic pressures. 

Cell walls: Most, but not all, prokaryotes possess a cell wall and some number of other external structures. A cell wall, if present, is often complex, consisting of many layers. Minimally, it consists of peptidoglycan, a polymer composed of a rigid network of polysaccharide strands cross-linked by peptide side chains. The cell wall maintains the shape of the cell and protects the cell from swelling and rupturing in hypotonic solutions, which are commonly found in the environment. In bacteria, the structure of the cell wall can be used as the basis of differentiating between gram-positive and gram-negative bacteria. 

Arachae do not possess peptidoglycan, but some have a similar structure called pseudomurein. 

–Gram Positive Cell Walls: The thick peptidoglycan layer encassing gram positive bacteria traps crystal violet dye, so the bacteria appear purple in a gram stain. The gram positive cell wall is much simpler than the gram engative cell wall. The gram positive cells wall is compsed of a single, thick layer of peptidoglycan, molecuels of lipoteichoic aid and teichoic acid are embedded in the wall and exposed on the surface of the cell.

–Gran Negative Cells Walls: The gram negative cell wall is composed of multiple layers. The peptidoglycan layer is thinner than in gram positve bacteria and is surrounded by an additional membrane composed of lipopolysaccharide. Porin proteins form aqueous pores in the oter membrane. The space between the outer membrane and the peptidoglycan is called the periplasmic space. 

Capsules and slime layers: In some bacteria, an additional gelatinous layer, the cpasule, surrounds the outer wall layers and can be detected by stiaing. A more loosely organized form of capsule that is harder to detect is called a slime layer. A capsule enables a prokaryotic cell to adhere to surfaces adn to other cells and to evade an immune response by interfering with recognition by phagocytic cells. Thus, a cpasule contribues to teh ability of some bacteria to casue disease. 

Falgella and pili; Some prokaryoties are motile. Many prokaryotic cells possess one falgellum at one end while others have one at each end of the cell. Some prokaryotic cells possess many flagella in clusters or dsitributed around the cell. 

Endospores: Some prokaryotes are able to form endospores, a thick wall around their geneomes and a small amount of cytoplasm when they are exposed to environmental stress. These endospores are highly resistant to environmental stress such as heat and when conditions imporve, they can germinate adn return to normal cell division to form vegetative cells after decades or even centuries of dormancy. The bacteria that cause tetanus, botulism and anthrax are all capable of forming spores. With a puncture wound, tetanus endosores may be driven deep into the skin, where conditions are favorable for them to gemrinate adn casue disease or even death. 

Nucleoid region: Prokaryotic cells do not package their chromosomes in a membrane bounded nucleus. Instead, theri circular DNA chromosomes are condensed to form a visible region of the cell called the nucleoide region. 

Plasmids: Many prokaryotic cells possess plasmids, which are small, extrachromosomal, independently replicating circles of DNA. Plasmids contain only a few genes, and although these genes may confer a selective dvantage, they are not essential for the cell’s survival.

Smaller Ribosomes: Prokaryotic ribosomes are smaller than eukaryotes and differ in protein and RNA content. Antibiotics such as tetracycline and chloramphenicol bind to prokaryotic rebosomes adn block protein synthesis but do not bind to eukaryotic ribosomes.

Lack of internal compartments: While neither bacteria nor archaea have consistent internal compartments found in all cells, they can have both lipid and protein bounded compartments. 

Horizontal Gene Transfer: In sexually reproducing populations, traits can only be trasnferred vertically form parent to child. Prokaryotes do not reproduce sexually; however, they can exchange DNA between different cells of the same species and in many cases, between cells of different species. This horizontal gene transfer occurs when genes move from one cell to another by conjugation requiring cell to cell contact by transduction which requires viruses and even by transformation where genetic material is picked up directly from the environment. 

–Transformation: Natural transformation occurs in some gram engative and gram positive species which are “competent”. Transformation occurs when one bacterial cell has died and ruptured, spilling its fragmented chromosomal DNA or palsmids into the environment. This DNA can be absorbed by anotehr cell and incorporated into its genome. 

–Transduction: is the transfer of DNA between prokaryotes by viruses. 

–Conjugation: Plasmids encode functions that are not necessary to the roganism but that provide a selective advantage in particualr environmetns. For example, antibiotic resistance is not necessary, but is advantageous in the presence of antbiotics. The best known trasmissible plasmid is the E. coli F plasmid (fertility factor). Cells cotnaining F plasmids are termed F+ or donor cells and cells that lack the F plasmid are F-or recipient cells. The F plasmid is an extrachromosomal piece of DNA that uses cellualr machinery for replication. After being tranferred fro a donor to a recipient cell, the F plasmid can integrate into the recipients cell’s genome by recombination. These are regions of homology with the E. coli chromosomes called insertion sequences (IS) adn recombinbation between the insertion sequences adn the chromosome integrates the F plasmid into the chromosome. Some conjugative plasmids can acquire antibiotic resistance genes, becoming resistance plasmids, or R plasmids. 

–CRISPR innate defenses: Prokaryotes use a variety of innate defenses against viral infection including restriction modification systems (the source of restriction endonucleases) and toxin-antitoxin systems. A structure of repeated sequences with “spacer regions” termed CRISPR for “clustered regularly interspaced short palindromic repeats” have also been identified which form a adaptive protection against viral infection. In response to viral challenge, bacteria and archaea will integrate short segments of viral nucleic acid in these CRISPR loci, then sue them to produce an RNA that can be used to guid a complex that degrades viral nucleic acid. 

–Metabolic Diversity: Prokarytoes not only have great metabolic diversity but also exhibit considerable metabolic flexibility which is not seen in any other group of organisms. Carbon is obtained in reduced forms by heterotrophs and in oxidized form (CO2) by autotrophs. Chemotrophs transform energy by oxidizing reduced chemicals obtained form the environment; phototrophs, on the other hand, transform energy by harvesting light. Lithotrophs obtain electrons from reduced inorganic substances in the environment, which organotrophs obtain electrons from reduced carbon sources. Prokaryotes can be classified into 5 different nutritional types and at times can even switch nturitional strategy based on nutritional needs and the avaiability of nutrients. This rarely, if even, occurs with eukaryotes.

One names a prokaryote nutritional strategy by stringing together into one word the terms that describe the approaches used to obtain carbon, electrons and energy. For example, with chemolithoheterotrophs, the source of energy and electrons is a reduced chemical in the environment. However, the chemical is inorganic not organic. “litho” means “stone” and so these organisms are known as “stone-eaters”. Photolithoautotrophs reduce atmospheric CO2 to produce molecules for biosynthesis. The source of elections for this reduction is inorganic.  Some prokarytoes use water as an electron source; however otehrs can use hydrogen and different forms of sulfur as electrons sources. Prokaryotic photosynthesis can differ significantly form green plant photosynthesis. Green plant photosynthesis uses water as a source of electrons and produces NADPH to drive the Calvin cycle. Regardless of the nutritional strategy used, any energy transformation msut ultimately convert one source of chemical potential energy intot he form of chemical potential energy usable by all living organisms: ATP. 

–Prokaryotes have diverse respirations and fermentations:

The transformation of energy in one chemcial potential energy source into usable source for the cell involves either phtosyntehsis, respriation or fermentation. Tehre can be significant differences in how prokaryotes and eukaryotes perform these processes. In eukaryotes, cellular respiration uses an electron transport chain to recycle electron donors into electron acceptors (primarily NADH and FADH2), reduce oxygen to water and produce a proton motive force to drive ATP synthesis. The final electron acceptor is oxygen, so these respirations are aerobic.

Prokaryotic respirations, on the other hand, show rgreat diversity of both eelctron donors and acceptors. Respriations that use a final electron acceptor other than oxygen are anaerobic respriations. Such acceptors include oxidized substances such as nitrate and sulfate. Some bacteria can even use carbon dioxide as an elector acceptor in a respiration, producing methane gas as a product. 

Fermentations may be used in a cell when a teminal electorn acceptor is not available to allow respiration. Fermentation can recycle reduced electron acceptors, such as NADH to their oxidized form, which is needed in oxidation reactions that drive the formation of small amounts of ATP. There is some diversity in the kinds of fermentations seen in eukaryotes: yeasts can ferment sugars to produce ethanol; animal muscle can ferment sugars to produce lactic acid and under certain conditions, plant cells can ferment sugars to produce ethanol. Prokaryotes, however, show much greater diversity of fermentations. A variety of metabolic pathways used by different prokaryotes can produce different alcohols and acids from fermentation of pyruvate, the product of glycolysis. Some of these products have industrial application and contribute to the flavorings of milk and cheese products. The production of chocolate is possible only due to the fermentation of coca. 

An unusal fermentation seen in prokaryotes is performed by teh Clostridium genus of bacteria. This genus includes species that are industrially valuable but also includes dangerous human pathogens.

C. tetani is the causative agent of tetanus and is introduced into the body most commonly through deep puncture wounds to the skin. The environment deep in a wound is anaerobic and C tetani can grow by fermenting the abundant amino acids in tissues. 

C. botulinum is a pathogenic bacteria producing “Botox” toxin used in cosmetic enahncements to reduce wrinkling of the skin. This bacteria can be introduced itno foods during the canning process and if an abudant source of prtoein is avaiable in the anaerobic interio of a can, the bacteria can ferment the constituent amino acids to support grwoth. Ingesting the toxin produced by the apthogen can lead to serius illness and even death. This pathogen is particularly dangeorus to young children with poorly developed gastrointestinal (GI) flora. 

Classification/Evolution:

The eukaryotes developed at least 2.7 billion years ago, following some 1-1.5 billion years of prokaryotic evolution. (Cooper, “The origin and evolution of cells” NCBI Bookshelf, “The cell: a molecular approach, 2nd edition, Sunderland (MA), Sinauer Associates, 2000).

Present day prokaryotes, which include all the various types of bacteria, are divided into two groups –the archabacteria and the eubacteria –which diverged early in evolution. Studies of their DNA sequences indicate that the archaebacteria and eubacteria are as different from each other as either is from present day eukarotes. Thus, a very early event in evolution appears to have been the divergence of 3 lines of descent from a common ancestor, giving rise to present day archaebacteria, eubacteria and eukaryotes. (Cooper, “The origin and evolution of cells” NCBI Bookshelf, “The cell: a molecular approach, 2nd edition, Sunderland (MA), Sinauer Associates, 2000).

Cyanobacteria: are the largest and most complex prokaryotes. Cyanobacteria bacteria are the bacteria in which photosynthesis evolved. (Cooper, “The origin and evolution of cells” NCBI Bookshelf, “The cell: a molecular approach, 2nd edition, Sunderland (MA), Sinauer Associates, 2000). 

Eubacteria: Some archaebacteria live in extreme envionrments, which are unusual today but may have been prevalent in primitive Earth. For example, thermoacidonphiles live in hot sulfur springs with temperatures as high as 80C and pH values as low as 2. The eubacteria include the common forms of present day bacteria –a large group of organisms that live in a wide range of environments, including soil, water, and other organisms (e.g., human pathogens). (Cooper, “The origin and evolution of cells” NCBI Bookshelf, “The cell: a molecular approach, 2nd edition, Sunderland (MA), Sinauer Associates, 2000).

Important Roles of Prokaryote:

Carbon fixation:

The role of photsyntehtic prokaryotes in fixing carbon is critcal in biogeochemical cyclin of carbon. The organic compoudns that plants, algae, and photsynthetic prokaryotes produce fro CO2 pass through food cahins to form the bodies of all the econsystem’s heterotrophs. Some prokaryotes, called emthanogens, can also contribute to reduce carbon in the environment by producing methane.Ancient cyanobacteria are thought o ahve added oxygen to the Earth’s atomsphere as a by produce of their photosynthesis to produce reduced carbon compounds. Modern photosynthetic prokartyoes that oxidize water continue to contribute to teh production of oxygen and are partly responsible for the reduction of atmospheric and soil CO2 levels.

Cycling of Nitrogen:

The ntigoren in the Earth’s atmosphere is in the form of nitrogen gas. The triple covalent bond that linds the two nitrogen atoms is not easy to break. Only a very few species of prokaryotes are able to accomplish this, reducing N2 to ammonia (NH3) which is used to build amino acids and other nitrogen containing biolgocial molecules. When the organisms thatcontain these moelcuesl die, decompasers return ntirogen to the soil as ammonia. This is then converted to nitrate (NO2-) by nitrifying bacterial, making nitrogen available for plants. The nitrate can also be converted back into molecular nitrogen by denitrifiers that retun the ntirogen to teh atomsophere completing the cycle. 

Transcription

Bacteria contain a single type of RNA polymerase. In contrast to eukaryotes, Bacterial RNA polymerase is able to initiate transcription in vitro without the help of additional proteins. The variable subunit of the RNA polymerase is called “sigma”. There are 5 subunits which make up the RNA polymerase which is referred to as the “holoenzyme”. Each type of promoter is recognized by its own sigma subunit.

 In bacteria, there are 2 sequences on the 5′ (upstream) side of the first nucleotide to be transcribed which serve as promoter sites. At -10 on the DNA template there is a  TATAAT sequence (“pribnow box”) and there is another sequence at the -35 region. 

Unlike eukaryotes, there is no  or of the mRNA transcript in prokaryotes.

Translation

In bacteria, the mechanism for selecting a start codon is a little different since bacteria have no . Instead, bacterial mRNA contains a specific ribosome binding site which is rich in A/G, called the Shine-Dalgarno sequence, located a few nucleotides upstream of the AUG start site of each coding region. This sequence base pairs with the 16S rRNA of the small ribosomal subunit to position the intiating AUG codon in the ribosome. This ability of the bacterial ribosome to assemble directly on a start codon AUG so long as a Shine-Dalgarno sequence precedes it means that bacterial mRNAs are often polycistronic in that they encode several different proteins, each of which is translated from the same mRNA molecule. This is not the case for eukaryotes. 

In prokaryotes, the initiation complex includes a special initiator tRNA molecule charged with a chemically modified methionine, N-formylmethionine. The initiator tRNA is known as tRNAfMet. The initiation complex also includes the small ribosomal subunit and the mRNA strand. The small subunit is positioned correclty on the mRNA dur to a conserved sequence in the 5′ end of the mRNA called the ribosome-binding sequence (RBS) that is complementary to the 3′ end of a small subunit rTNA. Once the complex of mRNA, initiator tRNA, and small ribosomal subunit is formed, the large subunit is added, and translation can begin. With the formation of the complete ribosome, the initiator tRNA is bound to the P site with the A site empty. 

Bacteria employ a rather unique trick to insure that incomplete mRNAs are not translated into proteins which could harm the cell. When the bacterial ribosome translates to the end of an incomplete RNA, a special RNA called tmRNA enters the A site of the ribosome and is itself translated into a special 11 amino acid tag to the C terminus of the truncated protein that signals to proteases that this protein should be degraded. Eukaryotes deal with this problem another way by recognizing the 5′ cap and the poly A tail before translation can start. 

Replication

In Procaryotes: the entire DNA replication unit is called a replicon. Procaryotic chromosomes contain 1 replicon whereas eucaryotic chromosomes contain many replicons. The protein assembly that begins DNA replication in procaryotes is referred to as a primosome. 

Each replicon contains an origin of replication where DNA replication starts. In E coli, for example, this origin (“OriC”) is a sequence of 245 bp which contains 3 nearly identical nucleotide sequences which are AT rich as well as 4 binding sequences further upstream for the dnaA protein which initiates the bending and unwinding of the template DNA. 

Since bacteria are circular, bacteria do not have the special problems of  where telomeres need to be added to the chromosome end.

Gene Regulation

Bacteria avoid making enzyme(s) of a pathway when substrate is absent, but are always ready to produce these enzymes if the substrate should appear in the environment. In this way, bacterial cells are able to adapt very quickly to any change in concentration of nutrients in their environment. The primary mechanisms that bacteria have evolved to minimize the energy cost for this type of on-and-off regulation is by grouping genes that encode enyzmes of a particular pathway in a structural unit called an operon. An operon is a group of genes adjacent to one another on the bacterial chromosome which are transcribed from a single promoter as one long mRNA molecule. 

Operons can be under either positive or negative control. Operons (or genes) under negative control are expressed, unless they are switched off by a repressor protein which will bind to a specific DNA sequence called the operator, making it impossible for RNA polymerase to initiate transcription at the promoter. Inversely, genes whose expression is under positive control will not be transcribed unless an active regulator protein is present which binds to a specific DNA sequence and assists the RNA polymerase in the initiation steps.

Lactose (lac) operon:

The lactose (lac) operon responsible for degradation of the sugar lactose in an inducibile operon because it functions only in the presence of an inducer (lactose here). The lac operon is also under negative regulation. In the absence of lactose, the operon is repressed by the binding of the repressor protein to the operator sequence, thus impeding the RNA polymerase function. Addition of lactose will, however, reverse this repression. (the repressor complexed with the inducer does not recognize the operator because of a conformation change in the repressor)

Full expression of the lac operon also requires a protein-mediated positive control mechanisms. In  E. coli a protein called CAP forms a complex with cAMP acquiring the ability to bind to a specific DNA sequence present in the promoter. The CAP-cAMP complex enhances binding of RNA polymerase to the promoter, thus allowing an increase in the frequency of transcription initiation.

This dual combination of positive and negative control allows E. coli to use alternative carbon sources such as lactose when glucose is absent. Falling levels of glucose induce an increase in cyclic AMP which binds to the CAP protein enabling it to bind to its specific DNA sequence near target promoters and thereby turn on the appropriate genes. But it would be wastful for CAP to induce expression of the lac operon if lactose is not present. So as a negative control, bacteria uses the lac repressor above to shut off the lac operon in the absence of lactose. The combination of both this positive and negative control acts as a type of genetic switch to make sure that the lac operon is off when lactose is not available and also that it is off when glucose is available. For the operon to be on, the cell needs -glucose and + lactose. 

Most of the routinely employed expression vectors fely on the lac control in order to overproduce a gene of choice. The lac promoter/operator functions as it does due to the interplay of three main components. First, the wild-type lac 10 region (TATGTT) is very weak. c-AMP activated CAP protein is able to bind to the CAP site just upststream of the –35 region which stimulates binding of RNA polymerase to the weak -10 site. Repression of the lac promer is observed when gluose is the main carbon source because very little c-AMP is present whihc results in low amounts of available c-AMP activate CAP protein. When poor carbon sources such as lactose of glycerol are used, c-AMP levels rise and large amounts of c-AMP activated CAP protein become availalbe. Thus induction of the lac promoter can occur. Second, Lac repressor binds to the lac operator. Lac repressor can be overcome by alloactose which is a natural byproduct of lactose utilizaiton in the cell or by the gratuitous inducter, IPTG. Third, the lac operator can form stable loop structures which prevents the initiation of transcripton due to the interaction of the Lac repressor with the lac operator (O1) and one of two auxiliary operators, O2, which is located downstream of the coding region of the lacZ gene, or O3 which is located just upstream of the CAP binding site. In summary, DNA binding sites include the operators O3 and O1, catabolite gene activator protein (CAP), the -35 site and the -10 site. Important RNA protein sites include the LacI translation stop site (TGA), the +1 lacZ transcription start site, the Shine Delgarno (SD) ribosome binding site for lacZ and the LacZ translation start site (ATG). (Altman (US 2012/0059145)

Tryptophan operon:

The tryptophan operon which contains the structural genes necessary for tryptophan biosynthesis is also under dual transcription control mechanisms. Again, it is under negative control in that an active repressor can bind to the operator blocking any transcription of the trp mRNA by the RNA polymerase. But here tryptophan is a corepressor rather than an inducer in that its presence changes the conformation of an inactive repressor protein which is then able to bind the operator. The trp operon is also under the control of an attenuation-antitermination mechanism (the leader mRNA possesses 4 repeates which can pair differently according to tryptophan availability, leading to an early termination of transcription of the operon or its full transcription.

Genetic Exchange between Bacteria:

4 types of genetic exchange occur among bacteria:

• transformation where bacteria uptake DNA. This does not occur frequently in nature but transformation is commonly used in the laboratory. E. Coli can take up DNA by transformation if they are made “competent” with calcium or magnesium. 

• transduction is the transfer of bacterial DNA from one cell to another by means of a bacteriophageinfection. Bacteriophages are viruses which infect bacteria. Their life cycle can be either lytic where they replicate and cause cell lysis or lysogenic where they integrate into the host chromosome. Transduction can either be  1) specialized where only specific genes adjacent to the site of integration are transferred along with the phage genome or 2) generalized which results from a random and accidental packaging of host DNA into the phage capsid. Thus generalized transducing particles should contain all or nearly all bacterial DNA and little or no phage DNA. 

• conjugation where DNA (usually plasmids) are exchanged between bacterial cells. This is a common mechanisms of genetic exchange between bacteria. This transferred DNA can either be integrated into the recipient chromosome or stably maintained as a plasmid and passed on to daughter bacteria as an autonomously replicating unit. 

• Transposons are segments of DNA which are able to move from one position to another in the genome or from the chromosomal DNA to a plasmid or the reverse. The simplest ones contain inverted repeats at each of their ends. Complex transposons usually code for antibiotic resistance and can contain transposases that excise and integrate the transposon into a new site.

Internal organs characteristic of vertebrates includes a liver, kidneys, and endocrine glands. All vertegrates have a heart and a closed circulatory system.

Endocrine glands: secrte hormones that help regulate many of the body’s functios.

Epithelium: is a basic tissue type that lines all body surfaces, cavities and tubes. All epithelia are supported by an avascular connective tissue layer called the  which contains  and  Epithelium is classified according to shape as follows:

• simple squamous epithelium: is 1 layer and flat. 

• simple cuboidal epithelium: is 1 layer and square; The ovary is simple squamous to cuboidal

• simple columnar epithelium: is 1 layer and columnar; lines most of digestive track, oviduct/fallopian tube (where  occurs), uterus.

• stratified squamous epithelium: is more than 1 cell layer and flat. Examples include the skin, vagina

Organs & Tissues derived from 

Integument/skin: Skin consists of two main parts: the epidermis on the outside and a lower layer of connective tissue which includes the two layered dermis. Skin is sometimes categorized as either thick such as that found on the foot or palm of the hand or thin. Thick skin has 5 layers in the epidermis whereas thin skin contains 4 layers. The various cells of the skin are attached to each other through type junctions and to the basement membrane through 

• epidermis is made up of a stratified (multilayed) squamous (flattened) epithelium composed largely of  The epidermis is renewed by  lying in its basal layer. Other cells associated with the epiermis are merkel cells which function as mechanoreceptors and langerhan cells which are phagocytic and present processed antigens to .

• dermis consists of the 1) papillary layerwhich is a loose connective tissue with fine  fibers and 2) reticular layer. 

Hair and sweat glands which penetrate into the dermis are actually down growths from the epidermal layer. Glands can have ducts (exocrine) or no ducts (endocrine). Sweat glands are made up of a cuboidal (shaped like a cube) epithelium surrounded by myoepithelial cells. One modified type of sweat glands are the mammary glands whose growth and development of the epithelium of the glands is regulated by steroid hormones. 

Sensory Epithelium:The sensory epithelium of the eye and ear do not regenerate while the olfactory epithelium will regenerate.

(1) Neural retina: consists of several cell layers.  lie closest to the external world so that light must pass through them to reach the photoreceptor cells which are classified as rods or cones which contain different rhodopsins. Rods are especially sensitive at low light levels while cones deter color and fine detail. Photoreceptors, like auditory hair cells, are permanent cells that do not divide and thus are not replaced if destroyed but the rhodopsin molecules are continually replaced.

(2) Ears: are the sensory epithelium responsible for hearing. Ears have auditory hair cells with protruding microvilli which held in an elaborate epithelial structure of supporting cells and overlaid by a mass of extracellular matrix. The hair cells convert mechanical stimuli into electrical signals. Sounds vibrations tilt the microvilli and open or close gated ion channels . The flow of electric charge carried into the cell by the ions alters the membrane potential and controls the release of neurotransmitter at the cell’s basal end, where the cell synapses with a nerve ending. Auditory hair cells, unlike olfactory neurons have to last a lifetime.

(2) Olfactory epithelium of the nose: contain . Basal stem cells in the epithelium generate replacements for the olfactory neurons that are lost. 

Organs & Tissues derived from 

Simple Columnar Epithelium of the Digestive Track: is made up of secretory mucous cells, absorptive cells as well as stem cells.

Colon: is a simple columnar epithelium whose function is water absorption. The colons has goblet cellswhich sythesize and secrete mucus which is a fecal lubrication.

Liver: is composed of two major types of differentiated epithelial cells: hepatocytes, cloated in the hepatic parenchymal plates, and biliary epithelial cells located in the bile ducts. Both of these differentiated lineages are dervied embryonically from a common founder cell, the hepatoblast, a derivative of the endoderm of the ventral foregut (Coleman, J. Pathology, 142(5), 1993).

Lungs: are formed from an outpocketing of the gut lining in the embryo. Repeated branching of a system of tubes terminate in several hundred million air filled sacs called alveoli which which contain .  which engulf foreign matter and bacteria are associated with the lungs.

Lungs: is the site where nutrients that have been absorbed from the gut and then transferred to the blood are processed by hepatocytes. Liver cell loss stimulates liver cell replacement.

Organs & Tissues derived from 

Blood vessels: are lined with endothelial cells. New vessels originate as capillaries which sprout from existing small vessels in response to specific signals in a process called angiogenesis. Angiogenesis is stimulated by hypoxia which results in the release of growth factors. Stimulation of cells around endothelial cells called pericytes may play an important role in the process.

kidney: The kidney filters plasma and excretes soluble waste products of metabolism. To prevent the los of serum proteins in the urine, the kidneys have a size selective barrier at the level of the glomeruli, the proximal protion of nephrons. The epitehlial cells (podocytes) of the glomerulus have processes (pedicles) that interdigitate to form a comb-linke structure through which serum is filtered and which excludes macromolcules of 70 kDa and alrger. Thus, two of the most abudnatn serum proteins, albumin and IgG are excluded form the priamry urine. After glomerular filtration the primary urine flows downstream to the tubular portiosn of the nephron. The proximal convoluted tubule (PCT), located immediately distal to the glomerulus, is reponsible for the reabsorption of mlus: is a key structural and functional element of the kidney.

–Glomerus is a key structural and functional element of the kidney. Each glomerulus is found as part of a larger structure that serves as the main functional unit of the kidney and is called a nehpon. About a million nephrones are found in each kidney. Each glomerulus is a network of up to fifty parallel capillaries encased in a structure known as Bowman’s capsule. The area inside Bowman’s capsule that is not taken up by the glomerular capillaries is known as Bowman’s space. The glomerulus functions as a filter, separating water and certain solutes from teh proteins and cells of the blood into Bowman’s space for futher processing in the conoluted tubules, loop of Henle, and collecting duct of the nephron.  (US63555245)

—-Glomerului are specialized renal capillary tufts which carry out the fitration of the plasma. Under normal conditions, the glomerular ultrafiltrate and ruine contain little if any protein. Glomerular disease (glomerulonephritis) is characterized by an increase in the permeability of the glomerular basement membrane (GBM), the primary ultrafiltration barrier restricting the passage of plasma proteins into the urine.

See also Kidney Dieases?

Muscle: There are 3 types of muscle 1) skeletal (which is attached to bones and responsible for skeletal movements is composed of ), 2) smooth (composed of  and found in organs like blood vessels, the GI tract) and 3) cardiac.

Cartilage and Bone: is considered a 3rd connective tissue (the other two being blood and muscle). Cartilage consists of chondrocytes. Bone matrix is secreted by .

Organs/Characteristics of Other Vertebrates:

Amphibians: 

Most amphibians have moist skin and msut remain in moist places to avoid drying out. Reptiles have dru, watertight skin. A layer of sclaes covers their bodies, greatly reducing water loss. These scales develop as surface cells fill with deratin, the same protein that forms claws, fingernails, hair and bird featehrs.

Amphibians breath by squeezing their throat to pump air into their lungs; this limits their breating capacity to the volume of their mouths. Reptiles developed pulmonary breathing, expanding and contracting the rib cage and diaphragm to suck air into the lungs and then force it out. The capacity of this system is limited only by the volume of the lungs.

Fish: Fishes are water dwelling creatures and must extract oxygen dissolved in the ater. They do this by directing a flow of water thorugh their mouths and accross their gills.

Fishes are unable to synthesize the aromotic amino acids (phenylalanine, tryptopah and tyrosine). Thus, they must consume them in thier foods.

See also receptors

The nuclear receptor superfamily is a large superfamily whose ligands are small hydrophobic signal molecules which diffuse directly across the plasma membrane and bind to these intracellular receptor proteins. These signal molecules include steroid hormones, thyroid hormones, retinoids and vitamin D.

Nuclear receptors can be subdivided into 3 groups, depending on the source and type of their ligand.

• Classical Steroid hormone receptors. The ligands for these receptors are exclusively from endogenous endocrine sources which are regulated by negative feedback control through the hypothalamus pituitary axis. After synthesis steroid hormones are circulated in the body to their target tissues where they bind their receptors with high affinity. The receptors regulate a variety of crucial metabolic developmental events, including sexual differentiation.

• Adopted Orphan nuclear receptors whose ligands are lipids which bind with lower affinity than the classical receptors. These receptors activate a feed forward, metabolic cascade that maintains nutrient lipid homeostasis by governing the transcription of a common family of genes involved in lipid metabolism, storage, transport and elimination. Adopted orphan nuclear receptors function as heterodimers with theretinoid X receptor (RXR)

• VDR/TR/RAR/EcR-RXR Heterodimers are 4 other RXR heterodimer receptors which includes vitamine D (VDR), thyroid hormones (TR), retinoic acid (RAR) and ecdysone (EcR). The ligands for these 4 receptors and the pathways they regulate employ elements of both the endocrine and lipid sensing receptor pathways.

• Nuclear receptors are all structurally related and contain the following domains:

  • A/B region at the NH2 terminal region which harbors a transcriptional activation function (AF-1).
  • C region DNA binding domain is the most conserved region and contains two highly conserved zinc finger motifs that target the receptor to specific DNA sequences.
  • D or hinge region that permits protein flexibility to allow for simultaneous receptor dimerization and DNA binding.
  • E region which is a large COOH terminal region that encompasses the ligand binding domain, dimerization interface and ligand dependent activation function. (AF-2). The E region is the hallmark of nuclear receptors and separates NRs from other sequence specific transcriptional factors.

  Mechanism of Action

  Upon ligand binding, nuclear receptors undergo a conformational change that coordinately dissociates corepressors and facilitates recruitment of coactivator proteins to enable transcriptional activation. Transcriptional Cofactors for NRs include 3 main types:

  • Enzyme containing co-activators are usually acetyl transferase, methyl transferase, kinase, ATPase, ubiquitin ligases or SRCs (steroid receptor co-activator) such as p160 SRC.
  • Mediator complexes which contain no enzyme activity such as the TRAP complexes.
  • Co-repressor complexes which are associated with histone deacetylase (HDACs).

Hemorheology  is the science of blood circulatory flow mechanics. It is important with respect to abnormal blood physiologic function, disease, premature fatigue or reduced performance following exposure to non-disease related stress such as exercise. Circulatory flow mechanics comprises a complex interaction of multiple pathways that can give rise to a hemorheologic abnormality such as an increase in a blood viscosity determinant, an increase in phosphatidlyserine exposure, or an increase in the expression of adhesion molecules on the surface of blood or endothelial cells.

Hemorheologic determinants (factors which influences circulatory flow mechanics) include a (1) blood viscosity determinant, (2) phosphatidylserine exposure and (2) expression of adhesion molecules on the surface of blood or endothelial cells. A hemorheologic abnormality refers to an abnormal level of a hemorheologic determinant in a subject. Hemorheologic abnormalities result in reduced blood flow, increased resistance to blood flow and tissue oxygen deficit in the systemic system or hypertension in the pulmonary system leading to systemic or pulmonary pathology or pathophysiology or premature fatigue or reduced performance.

(1) a blood viscocity determinant is a conventional term used by hemorheologists to refer to factors which, if altered, can increase blood viscosity to abnormal levels. The most common blood viscosity determinants include (a) red blood cell concentration, (b) red blood cell aggregation, (c) red blood cell rigidity (resulting in reduced deformability), (d) plasma viscosity, and (e) abnormal red blood cell shape (e.g., formation of echinocytes, stomatocytes or elliptocytes).

(a) Hematocrit (Hct) is the prime determinant of blood viscosity. The more cells, the greater the viscosity. Unlike that of exercising humans, the Hct of exercising horses increases to polycythemic levels. This is because unlike the human spleen, the equine spleen sequesters nearly half the total erythrocyte mass. Upon exercise, it mobilizes the sequestered erythrocytes into the circulation which increases blood viscosity.

(b) blood changes its configuration as it flows in the circulation; particles in the central axis of vessels travel fastest. Shear rate (proportional to velocity of flow) differs throughout the circulation depending upon the vessel diameter and blood flow velocity.

(c) Deformability lowers blood viscosity and provides erythrocytes with a property that allows them to pass through channels much smaller than their own diameter. On the other hand, increased reigidity reduces the ability of the cell to bend its membrane, causing the red blood cell to lose its biconcave shape and preventing the red blood cell from deforming.

(d) The only constituents of plasma that have an effect on blood viscosity are fibrinogen and macromolecular globulines (e.g., IgG, IgA and IgM).

(e) Echinocytes are rigid cells due to a decreased surface area-to-volume ratio which occurs because the tips of spicules bud off and reduce their surface area. Their rigidity causes an impeded blood flow and reduces tissue oxygenation in much the same way as do sickle cells. Another examples of an abnormally shaped red blood cell is the stomatocyte characterized by a pale, elongated, mouth-like area in the center of the cells. Another abnormally shaped red blood cell is the elliptocytes or ovalocytes which appear oval or elongated in shape and are rich in hemoglobin.

(2) Phosphatidylserine Exposure: Membranes of normal erythrocytes contain 4 major phospholipid classes districtued asymmetrically between lipid bilayers; Phosphatidylcholine (PC) and sphingomyelin (SM) localize mainly in the outer bilayer. Phosphatidylethanolamine (PE), however, resides mainly in the inner bilayer, while phosphatidylserine (PS) resides exclusively there. Normal biconcave erythrocytes transform into echinocytes after a membrane perturbation induces phospholipid redistribution and causes PS expression on the cell’s surface.

(3) adhesion molecules: blood cells (RBCs, platelets, leukocytes), endothelial cells and plasma contain adhesion molecules which, when stimulated, interact with their individual specific receptors and reversibly bind cells-to-cells, cells-to-protein, and protein-to protein. With respect to the cell adhesion type (blood cells-to-blood cells, for example), adhesion molecules include an immunoglobulin (e.g., IgG, IgA, IgM), a thrombospondin protin, a fibronectin protein etc). With respect to blood cells-to-endothelial cells, adhesion molecules include I-CMA-1, an integrin protein, a selectin protein, a cadherin protein a cluster of differentiation (CD35, CD36), etc.

The term hemorheologically-active compound refers to a compound that improves blood flow by reducing an abnormal level of a hemorheological determinant.

Structure of Lipid Droplets:

Lipid droplets are organelles with a different structure form the rest of the endomembrane system. They consist of a netral lipid core surrounded by a single alyer of phospholipid. Neutral lipids are hydrophobic and include triglycerides and sterol lipids. These neutral lipids are made soluble in the aqueous cytosol by being coated with a phospholipid. 

Functions: 

Lipid drops form storage depots for lipids taht are used for energy metabolism, and to form membranes. Lipid droplets can also contain proteins involved in lipid syntehsis. This allows them to act as a seocndary site of lipid syntehsis. 

There is a bidirectional flow of proteins through the nucleus. tRNAs and mRNAs are synthesized, for example, in the nucleus and transported out to the cytosol. Vice versa, proteins like histones, DNA and RNA polymerases, gene regulatory proteins, and RNA processing proteins are imported into the nucleus from the cytosol. 

The nuclear envelope encloses the DNA of a eucaryotic cell. The envelope consists of an inner nuclear membrane that contains specific proteins that act as binding sites for chromatin and for the protein meshwork of the nuclear lamina that provides structural support for the nuclear envelope. The inner membrane is surrounded by an outer nuclear membrane which is continuous with the membrane of the .endoplasmic reticulum. The envelope consists of two membranes that are penetrated by nuclear pores. 

Each nuclear pore contains one or more aqueous channels through which small water soluble molecules can passively diffuse. Large molecules (above 17K daltons) are generally unable to diffuse the channels (which are about 9nm wide). Thus large molecules like ribosomal subunits are unable to be exported and molecules like polymerases are unable to be imported into the nucleus using simple diffusion. Instead, such molecules must rely upon specific receptor proteins that transport them through nuclear pore complexes. A single pore complex can conduct traffic of proteins which move both into and out of the nucleus. Not all types of proteins are, however, imported and exported into the nucleus. The process is a selective one which is controlled by either signal sequences or patches on the proteins which are either imported or exported.

Localization: Nuclear localization signals (NLSs) which are rich in positively charged amino acids like lysine and arginine are present only on proteins being imported into the nucleus. Such NLS are recognized by nuclear import receptors

Nuclear export signals which bind to their complementary nuclear export receptors determine which proteins are exported out of the nucleus. 

In many cases, transport of nuclear proteins depends on the regulation of nuclear localization and export signals which are turned on or off, typically by phosphorylation. 

Both the import and export of proteins through the nuclear pore complex requires energy which is provided by the hydrolysis of GTP by the GTPase Ran which can exist in 2 conformational states depending on whether GDP or GTP is bound. Conversion between the 2 states is provided by a cytosolic GTPase-activating protein (GAP) that triggers GTP hydrolysis and a nuclear guanine exchange factor (GEF) that promotes the exchange of GDP for GTP.

In nuclear import, the Ran-GDP and the protein with its nuclear localization signal come together with the nuclear import receptor, the import receptors then move with their bound cargo into the nuclear side of the pore complex where Ran-GTP binding causes the the import receptors to release their cargo. The now empty import receptor with Ran-GTP bound is transported back through the pore complex to the cytosol where Ran-GTP is converted back to Ran-GDP to complete the cycle. Nuclear export occurs by a similar mechanism exept that Ran-GTP in the nucleus promotes cargo binding to the export receptor and the export receptor releases both its cargo and Ran-GDP in the cytosol where it is hydrolyzed by Ran-GAP. 

The transport of nuclear proteins through nuclear pore complexes is different from the transport of proteins across membranes of other organelles because it occurs through large aqueous pores rather than through a protein transporter in one or more lipid bilayers. Because of this, proteins can usually be transported from a pore complex in their fully folded conformation. Moreover, Nuclear translocation signals are not cleaved off after transport into or out of the nucleus. This is not the case with other membrane bound organelles where the signal sequence is often removed after protein translocation.

Lysosomes are digestive vesicles that arise from the Golgi apparatus. They contain high levels of a vareity of enzymes that can degrade proteins, nucleic acids, lipids and carbohydrates. The lysomesal enzymes break down old organelles and reclce their component molecules. In addiiton to breaking down organelles and other structures within cells, lysomes eliminate other cells that the cell has engulfed by phagocytosis. When a white blood cell, for example, phagocytoses a passing pathogen, lysosomes fuse with the reuslting food vesicle, rleasing their enzymes into the vesicle and degrading the material within. 

Optimally active at acid pH:

Lysosomes are membrane enclosed compartments filled with acid hydrolytic enzymes. A H+ pump in the lysosomal membrane uses the energy of ATP hydrolysis to pump H+ into the lysosome thereby maintaining the lumen at its acidic pH of about 5.0. 

Digestive enzymes are delivered to lysosomes via the Golgi apparatus. Substances to be digested come from endocytosis.

Delivery of hydrolases and membrane proteins: are synthesized in the rough ER and transported through the Golgi apparatus to transport vesicles that deliver these proteins to late (which will form lysosomes). Lysosomal hydrolases have a unique marker in the form of mannose 6-phosphate (M6P) groups which are added exclusively to the N-linked olgiosaccharides of these enzymes as they pass through the lumen of the cis Golgi. 2 enzymes are responsible for adding the M6P groups and these enzymes recognize the hydrolase proteins due to a signal patch on the polypeptide surface of the hydrolase. 

The M6P groups are recognized by transmembrane M6P receptor proteins which are present in the trans Golgi which aid in packaging the hydrolases into clathrin coated vesicles that bud from the trans Golgi. The receptor travels with the vesicle to a late endosome where the hydrolase dissociates from the receptor due to the lower pH in the endosome. The receptor is then returned to the golgi in a vesicle where it can be reused. 

Sources of substances to be digested: 1) endocytosis is the process by which cells take up macromolecules. 2 types of endocytosis are distinguished based on the size of the endocytic vesicles formed. Phagocytosisinvolves the ingestion of large particles such as microorganisms or dead cells via phagosomes and pinocytosis involves the ingestion of solutes via small pinocytic vesicles. In mammals, 3 types of white blood cells are phagocytes; . Eucarytoic cells continually ingest parts of their plasma membrane in the form of small pinocytic (endocytic) vesicles. The same amount of membrane removed is restored through the process of exocytosis. Pincocytic vesicles are typically clathrin coated although they may also be caveolae.

Many cell surface receptors that bind specific extracellular macromolecules become localized in clathrin coated pits in a process called receptor mediated endocytosis. (examples include LDL receptors) The coated endocytic veiscles rapidly shed their clathrin coats and fuse with early endosomes. Most of the ligands dissociate from their receptors in the acidic environment of the endosome and end up in lysosomes while most of the receptors are recycled back to the cell surface but sometimes both the receptor and ligand end up being degraded in lysosomes, resulting in receptor down regulation. In some cases, both are transferred to a different plasma membrane and the ligand is thereby released by exocytosis at a surface of the cell different from that where it started in a process called transcytosis.

Lysosomal storage Disorders:

A number of human genetic disorders affect lysosomes.

Tay-Sachs disease: is caused by the loss of function of a single lysosomal enzyme (hexosaminidase). This enzyme is necessary to break down a membrane glycoolipid found in nerve cells. Accmulation of glycolipid in lysosomes affects nerve cell function, leading to a vareity of clinical symptoms such as seizures and musle rigidity.